It probably depends on the kinds of projects you do, but this kind of "halfway there" PCB seems like a lot of fuss for not a lot of gain. Why not just design the PCB the way you want it look for the final product, and then, in places where you'd still like to work with a breakout board or something, have jumpers (holes, really) so you can decide whether to let everything pass through the board as it would in the final product or whether it has to go someplace else? I see the author is answering the comments, so maybe they can explain?